One works with Lite, which is a single server backend, the other with LoadBalancing / PhotonCloud which is a multiserver, load balanced backend
Yes, you can run Photon - LoadBalancing instance even if you just host it on a single machine. it will still be 2+ 'servers' though independent of that.
The other one is the old library which existed since photon 1 already and prior to the LoadBalancing was used for 'room based' games
also multi server assembly server side development is quite a bit trickier than the Lite Application is